Post-translational modifications identified by elemental analysis

ABSTRACT

Methods and kits for enzymes involved in post-translational modifications are provided. The methods employ elemental analysis, including ICP-MS. The methods allow for the convenient and accurate analysis of post-translation modifications of substrates by enzymes involved in post-translational modifications, including kinase and phosphatase enzymes.

CROSS-REFERENCE TO RELATED APPLICATIONS This application claims priorityto U.S. Provisional Patent application 60/772,584 filed Feb. 13, 2006entitled, “POST-TRANSLATIONAL MODIFICATIONS IDENTIFIED BY ICP-MS”, theentire contents of which are herein incorporated by reference. COPYRIGHTAND LEGAL NOTICES

A portion of the disclosure of this patent document contains materialwhich is subject to copyright protection. The copyright owner has noobjection to the facsimile reproduction by anyone of the patent documentor the patent disclosure, as it appears in the Patent and TrademarkOffice patent files or records, but otherwise reserves all copyrightswhatsoever.

FIELD

This invention pertains to the determination of post-translationalmodification of proteins such as phosphorylation and dephosphorylation,including methods and kits, employing elemental analysis.

INTRODUCTION

The methods described facilitate high-throughput assays throughmultiplexing assays that until now have largely been performedindividually. The principal, but not exclusive, target of the method isto provide for the evaluation of agonists and antagonists tophosphorylation (kinase) and dephosphorylation (phosphatase), as theseare targets for pharmaceutical drug discovery applications.

Overall there are no less than 20 platform technologies available (forexample, Radioactivity, Fluorescence Polarization, Time ResolvedFluorescence, Fluorescence Resonance Energy Transfer¹, etc.), howevermost display important limitations for the development of a coherentscreening-profiling platform. Well known drawbacks include those relatedto heterogeneous assay systems, limitations in ATP concentration,compound interferences and limitations of substrate size and charge. Aswell these methods have low level of sensitivity and are difficult tomultiplex², i.e. assay dozens of different kinases/phosphatasessimultaneously. Thus there are many needs unfulfilled by the prior art,including but not limited to a need for a sensitive, robust andquantitative assay for protein post-translational modification. Further,there is a need for a multiplexed enzymatic assay that enables highthroughput operation.

Among the many advantages offered by the applicant's teaching are thefollowing: I. The assay can be applied to any type of protein kinase;II. The assay can be applied to any type of protein phosphatase; III.The assay does not exclusively rely on the use of antibodies (althoughsome embodiments might include antibodies); IV. The methods can be usedto detect and study protein kinase antagonists and agonists; V. Themethods can be used to study protein kinase signal transductioncascades; VI. The methods can be used with a number of different proteinkinase buffers; VII. The assay can be supplied as a kit; VIII. The assaycan be used to measure activity of multiple kinases/phosphatases in cellfree systems; IX. The assay can be used to determine activity ofmultiple kinases/phosphatases in cellular lysates; X. The assay can beused to determine various endogenous and transfected kinase activitieswithin intact cells.

Post-translational modifications of proteins are carried out by enzymeswithin living cells. Known post-translational modifications includeprotein phosphorylation and dephosphorylation as well as methylation,prenelation, sulfation, and ubiquitination. The presence or absence ofthe phosphate group on proteins, especially enzymes, is known to play aregulatory role in many biochemical pathways and signal transductionpathways. Hence together, specialized kinases and phosphatases regulateenzymatic activity.

A kinase function is to transfer phosphate groups (phosphorylation) fromhigh-energy donor molecules, such as ATP, to specific target molecules(substrates). An enzyme that removes phosphate groups from targets isknown as a phosphatase. The largest group of kinases are proteinkinases, which act on and modify the activity of specific proteins.Various other kinases act on small molecules (lipids, carbohydrates,amino acids, nucleotides and more) often named after their substratesand include: Adenylate kinase, Creatine kinase, Pyruvate kinase,Hexokinase, Nucleotide diphosphate kinase, Thymidine kinase.

Protein kinases catalyze the transfer of phosphate from adenosinetriphosphate (ATP) to the targeted peptide or protein substrate at aserine, threonine, or tyrosine residue. Protein kinases aredistinguished by their ability to phosphorylate substrates on discretesequences. Commercially available kinases can be in the active form(phosphorylated by supplier) or in the inactive form and requirephosphorylation by another kinase.

A protein phosphatase hydrolyses phosphoric acid monoesters atphosphoserine, phosphothreonine, or phosphotyrosine residue into aphosphate ion and a protein or peptide molecule with a free hydroxygroup. This action is directly opposite to that of the protein kinase.Examples include: the protein tyrosine phosphatases, which hydrolysephospho-tyrosine residues, alkaline phosphatase, the serine/threoninephosphatases and inositol monophosphatase.

“Protein kinase or phosphatase” as used in the invention may be natural,recombinant or chemically synthesized. If either natural or recombinant,it may be substantially pure (i.e., present in a population of moleculesin which it is at least 50% homogeneous), partially purified (i.e.,represented by at least 1% of the molecules present in a fraction of acellular lysate) or may be present in a crude biological sample.

“Enzyme (kinase, phosphatase) assays” may target principally one ofthree quantities: concentration (of either the enzyme or the substrateon which it works); activity of the enzyme on the substrate orsubstrates; and specificity of the enzymatic activity for a givensubstrate or suite of substrates. The assay is of value in thedetermination of the impact of agonists and antagonists on the activityand specificity of the enzymatic action. Examples of the type ofinformation that may be obtained from such assays include 1. Thespecificity of action on a suite of substrates can be determined if theenzyme is known to be present; II. The activity of the enzyme towardseach of a suite of substrates can be determined if the concentration ofthe enzyme and the time of interaction is known; III. The presence of anenzyme can be determined if action on a substrate is detected; IV. Theconcentration of the enzyme can be determined if the concentration ofthe substrate and the activity of the enzyme for that substrate and thetime of interaction is known.

“Specific kinase assay” refers to an enzyme assay specific forindividual kinases in the presence or absence of other phosphatases andkinases.

“Specific phosphatase assay” refers to an enzyme assay specific forindividual phosphatase in the presence or absence of other phosphatasesand kinases.

“Non-phosphorylated substrate” is biological material that may bephosphorylated by a protein kinase. The substrate which is targeted bykinases may be a structural protein or another enzyme which is afunctional protein or a peptide or a lipid. For example, proteinsubstrates that are typically used in an assay for specific kinaseactivity include milk casein; histones, isolated from calves;phosphovitin, isolated from egg yolks; and myelin basic proteins,isolated from bovine spinal cords. Production of peptides may beachieved by enzymatic digestion of full length proteins, chemicalsynthesis³ or expression of a recombinant peptide. Peptide substratesmay contain from about 6 to about 50 amino acids.

“Element tag” or “tag” is a chemical moiety which includes any elementalatom or multitude of elemental atoms having one or many isotopesattached to a supporting molecular structure. The element tag can alsocomprise the means of attaching the tag to a substrate. Differentelement tags may be distinguished on the basis of the elementalcomposition of the tags. A tag may contain many copies of a givenisotope and may have a reproducible copy number of each isotope in eachtag. An element tag may be distinguishable from a multitude of otherelement tags in the same sample because its elemental or isotopiccomposition is different from that of other tags. For example, theelement tag could be a metal-chelate polymer with an attachment group.The element can be selected from a group consisting of the noble metals,lanthanides, rare earth elements, transition elements, gold, silver,platinum, rhodium, iridium and palladium. The element can be an isotope.The element can include more than one atom of an isotope. For example,an elemental tag can be a metal-chelate polymer with an attachmentgroup. As is known to those skilled in the art, an element tag can be anatomic part of chemical moiety, such as for example Ti in a titaniumdioxide particle.

A “support” is a surface which has been functionalized by, for example,pyrrole-2,5-dione (maleimido), sulfonic acid anion, or p-(chloromethyl)styrene. A support, for example, may be but is not limited to, asynthetic membrane, bead (polystyrene, agarose, silica, etc), planarsurface in plastic microwells, glass slides, reaction tubes, etc. as isknown to those skilled in the art.

Element labeled bead” is a type of support bead (polystyrene, agarose,silica, etc) which functionally incorporates or is imbibed with anelement or multitude of elements with one or many isotopes. As is knownto those skilled in the art, an element can be an atomic part ofchemical moiety, such as for example Ti in titanium dioxide.

“Uniquely labeled bead” refers to a physical entity that includes amultitude of atoms of one or more isotopes of one or more elementsimbibed in a bead such that one type of said bead labeled with one ormore isotopes or elements is distinguishable from other types of saidbeads labeled with distinguishable elements or isotopes by elementalanalysis. Each uniquely labeled bead can bear a multitude of substratesspecific for a given enzyme.

A “substrate labeled with an element” tag is a substrate which hasincluded an element tag which allows the substrate to be determined byelemental analysis.

A “substrate labeled with a unique element tag” is a substrate labeledwith an element tag that is distinguishable from a multitude of otherelement tags in the same sample and whose presence is indicative of thesubstrate specific to that tag.

A “free phosphorylated substrate” is a substrate that is phosphorylatedafter synthesis or synthesized using phosphorylated amino acids.Phosphorylamino acids for incorporation into chemically synthesizedpeptides may be obtained from numerous commercial sources as is known tothose skilled in the art.

A phosphorylated substrate is distinguished from a non-phosphorylatedsubstrate primarily by the presence of a phosphate group.

“Metal ion coordination complex” is an association of a central metalion and surrounding ligands, in particular transition metal, rare earthand other metal (Ga(III), Fe(III), Al(III), Sc(III), Lu(III), Th(III),Zr(IV), complexes, for example, but not limited to, of iminodiaceticacid (IDA) or nitrilotriacetic acid (NTA). Metal oxide forms (such asTi02, Zr02, indium tin oxide) are metal compounds with coordinatingproperties for phosphate ions relevant to the present invention. Thesehave been widely adopted in biology, and are gaining increasing use inbiotechnology, particularly in the protein purification technique knownas Immobilised Metal-ion Affinity Chromatography (IMAC).

Reactions are allowed to proceed for various durations and at differenttemperatures. The reaction conditions vary depending on the specifickinase/phosphatase, as is known to those skilled in the art. For manymammalian kinases, the reaction is carried out at room (25° C.) orelevated temperatures, usually in the range of 20° C. to 40° C. Forhigh-throughput applications, reaction time is minimized, and is usuallyfrom 10 minutes to 4 hours, more usually about 10 minutes to 1 hour.

“Elemental analysis” is a process where a sample is analyzed for itselemental composition and sometimes isotopic composition. Elementalanalysis can be accomplished by a number of methods, including but notlimited to: I. Optical atomic spectroscopy, such as flame atomicabsorption, graphite furnace atomic absorption, and inductively coupledplasma atomic emission, which probe the outer electronic structure ofatoms; II. Mass spectrometric atomic spectroscopy, such as inductivelycoupled mass spectrometry, which probes the mass of atoms; III. X-rayfluorescence, particle induced x-ray emission, x-ray photoelectronspectroscopy, and Auger electron spectroscopy which probes the innerelectronic structure of atoms.

“Elemental analyzer” is an instrument for the quantitation of atomiccomposition of a sample employing one of the methods of elementalanalysis.

“Particle elemental analysis” is a process where an analyzed sample,composed of particles dispersed in a liquid (beads in buffer, forexample), is interrogated in such manner that the atomic composition isrecorded for individual particles (bead-by-bead, for example).

“Solution (volume) elemental analysis” is a process where an analyzedsample is interrogated in such manner that the atomic composition isaveraged over the entire volume of the sample.

“Transition element” means any element having the following atomicnumbers, 21-29, 39-47, 57-79 and 89. Transition elements include therare earth elements, lanthanides and noble metals (Cotton and Wilkinson,1972).

“Affinity product” or “affinity reagent” refers to biological molecules(for example, but not limited to antibody, aptamer, lectin,sequence-specific binding peptide, etc) which are known to form highlyspecific non-covalent bonds with respective target molecules (peptides,antigens, small molecules, etc). Affinity reagent labeled with a uniqueelement tag is an affinity product labeled with an element tag that isunique and distinguishable from a multitude of other element tags in thesame sample.

Kinase reaction buffer—There are a number of examples of reactionbuffers formulated for specific kinases in the literature. The reactiongenerally requires the presence of an effective amount of a nucleosidetriphosphate, such as ATP, usually at a concentration in the range ofabout 0.01-20 mM. As is known to those skilled in the art, the buffermay contain substances such as HEPES or Tris-HCl, at a concentration inthe range of about 1-50 mM, at a pH of about 5-9. Individual enzymes maygenerally be present in an amount in the range of 1 pg-5 ng/μl. Cationssuch as Mg, Mn and Ca, at concentrations 0.1-5 mM may be employed. Otheradditives may include DTT at a concentration in the range of 0.1-2 mM.In some instances sodium ortho-vanadate may be used at a concentrationof about 0.5-2 mM to inhibit contaminating phosphatases. Also, an inertprotein may be included, such as ovalbumin, serum albumin, etc., at0.1-5 mg/ml, to prevent non-specific binding and inactivation of lowconcentration assay components, especially to prevent enzyme binding tothe surface. For some protein kinases, other cofactors may be requiredsuch as phospholipids, calmodulin, cAMP, phosphotidylserine, anddiolein, as is known to those skilled in the art.

Phosphatase reaction buffer is a solution of Tris-HCl, at aconcentration in the range of about 50-100 mM, at a pH of about 8-9.5,and 100 mM NaCl. Individual enzymes may generally be present in anamount in the range of about 1 pg-5 ng/μl. Cations such as Mg, Mn andCa, at concentrations 1-5 mM may be employed. Other additives mayinclude DTT at a concentration in the range of 0.1-2 mM.

Methods of separation may include washing of the support by addition ofwashing buffer (may consist of a solution of 100-150 mM NaCl, 50-100 mMTris-HCl pH 7) and aspiration of said wash buffer from container (wellof a multiwell plate, microtube, etc). If assay if performed with a beadsupport or with element labeled beads, the method of separation mayinclude low speed centrifugation (300-9,300×g), with or withoutMolecular Weight Cut Off (MWCO) filtration devices.

Elution (of an element tag and/or a metal coordination complex) intosolution means (preferably quantitative) solubilization of the elementscomprising the tag and or metal atom(s) of the metal coordinationcomplex, in a form to allow solution elemental analysis. Elution mayinclude conventional elution buffers and solvents that maintain themolecular constructs intact, or may involve acid degradation or othermeans to convert the elements or metals of interest into solution orslurry as is known to those skilled in the art.

SUMMARY

These and other features of the applicant's teachings are set forthherein. An aspect of the applicant's teachings is to provide a methodfor a kinase assay, comprising: incubating ATP, at least one kinase, anda free non-phosphorylated substrate labeled with an element tag, with asupport having attached thereto metal ion coordination complexes underconditions to enable the kinase to phosphorylate the substrate;separating free non-phosphorylated substrate from bound phosphorylatedsubstrate labeled with an element tag to the support; eluting theelement tag associated with the resultant phosphorylated substrate intoa solution; and performing solution elemental analysis of said solution.

Another aspect of the applicant's teachings is to provide a method for aphosphatase assay, comprising: incubating free phosphorylated substratelabeled with an element tag with a support having attached thereto metalion coordination complexes; separating free phosphorylated substratefrom bound phosphorylated substrate labeled with an element tag attachedto the metal ion coordination complexes attached to the support;incubating ADP and at least one phosphatase with the boundphosphorylated substrate labeled with an element tag attached to themetal ion coordination complexes attached to the support underconditions to enable the phosphatase to dephosphorylate the substrate;separating free non-phosphorylated substrate labeled with an element tagfrom bound phosphorylated substrate attached to the metal ioncoordination complexes attached to the support; and measuring the tagelement in a solution of the free non-phosphorylated substrate.

Another aspect of the applicant's teachings is to provide a method for aphosphatase assay, comprising: incubating, in a multitude of solutions,each solution comprising a different free phosphorylated substratelabeled with an element tag, which can optionally be the same elementtag for all substrates, a plurality of element labeled supports havingattached thereto a metal ion coordination complex, in such manner thateach type of phosphorylated substrate labeled with an element tag, whichcan optionally be the same element tag for all substrates, is attachedto a single type of element labeled support; separating freephosphorylated substrate from the bound substrate attached to the metalion coordination complex attached to the multitude of element labeledsupports in the multitude of separate solutions; incubating themultitude of element labeled supports having attached thereto themultitude of phosphorylated substrates labeled with an element tag,which can optionally be the same element tag for all substrates, throughattachment to the metal ion coordination complex that is attached to thesupports in a single solution with ADP and at least one phosphatase inconditions that enable the phosphatase to dephosphorylate thephosphorylated substrates; separating free non-phosphorylated substratefrom bound phosphorylated substrate labeled with an element tag, whichcan optionally be the same element tag for all substrates, attached tothe metal ion coordination complex attached to said multitude of elementlabeled supports; and performing particle elemental analysis of boundphosphorylated substrate labeled with an element tag, which canoptionally be the same element tag for all substrates, attached to themetal ion coordination complex attached to the multitude of elementlabeled supports.

Another aspect of the applicant's teachings is to provide a method for akinase assay, comprising: incubating ATP, at least one kinase, and afree metal ion coordination complex, with an immobilizednon-phosphorylated substrate under conditions which enable the kinase tophosphorylate the substrate; separating immobilized phosphorylatedsubstrate attached to the metal ion coordination complex from the freeion coordination complex and the immobilized non-phosphorylatedsubstrate; eluting the metal ion coordination complex attached to theimmobilized phosphorylated substrate into a solution; and measuring thesolution by elemental analysis.

Another aspect of the applicant's teachings is to provide a method for akinase assay, comprising: incubating ATP, at least one kinase, a freemetal ion coordination complex, and a multitude of non-phosphorylatedsubstrates immobilized on element labeled supports in such manner that asingle type of non-phosphorylated substrate is attached to a single typeof element labeled support, in conditions to enable the kinase tophosphorylate the substrates; separating the multitude of phosphorylatedsubstrates immobilized on element labeled supports having attached metalion coordination complex from the free metal ion coordination complexesand the multitude of immobilized non-phosphorylated substrates; andmeasuring the multitude of phosphorylated substrate immobilized onelement labeled supports having attached metal ion coordination complexby elemental analysis.

Another aspect of the applicant's teachings is to provide a method for akinase assay, comprising: introducing a multitude of non-phosphorylatedsubstrates with element tags into live cells; incubating the cellshaving the introduced non-phosphorylated substrates with an agonist oran antagonist of kinase activity; fixing and permeabilizing the cells;incubating the cells with element-labeled antibodies directed againstphosphospecific kinase substrates; separating the cells from unboundantibodies; and measuring the phosphorylated substrates with elementtags and attached element-labeled antibodies by elemental analysis.

Another aspect of the applicant's teachings is to provide a method for aphosphatase assay, comprising: incubating ADP and at least onephosphatase, with an immobilized phosphorylated substrate with attachedmetal ion coordination complexes in conditions that enable thephosphatase to dephosphorylate the substrate; separating the free metalion coordination complex from the immobilized non-phosphorylatedsubstrate and the immobilized phosphorylated substrate with attachedmetal ion coordination complex; eluting the metal ion coordinationcomplex into a solution; and measuring the solution by elementalanalysis.

Another aspect of the applicant's teachings is to provide a method forphosphatase assay, comprising: incubating ADP, at least one phosphatase,and a multitude of phosphorylated substrates with attached metal ioncoordination complex immobilized to element labeled supports in suchmanner that a single type of phosphorylated substrate is attached to asingle type of element labeled support in conditions that enable thephosphatase to dephosphorylate the phosphorylated substrates; separatingthe free metal ion coordination complex from the multitude ofnon-phosphorylated substrates immobilized to element labeled supportsand the multitude of immobilized phosphorylated substrate; and measuringthe metal ion coordination complex attached to the multitude ofphosphorylated substrate immobilized to uniquely labeled supports byelemental analysis.

Another aspect of the applicant's teachings is to provide a kit for thedetection and measurement of elements in a sample, where the measuredelements include an element tag attached to a non-phosphorylatedsubstrate and a metal ion coordination complex, comprising: an elementtag for directly tagging non-phosphorylated substrate;non-phosphorylated substrate; a solid support; a metal ion coordinationcomplex; and optionally, kinase; kinase buffer; and ATP. The kit canfurther comprise instructions for i) directly tagging thenon-phosphorylated substrate with an element tag; ii) incubating kinasewith element labeled non-phosphorylated substrate in kinase buffer, iii)attaching metal ion coordination complex to the support; iv) incubatingthe kinase with element labeled non-phosphorylated substrate in kinasebuffer with the support having attached metal ion coordination complex;v) separating bound substrate from unbound substrate; vi) eluting thebound substrate, and vii) detecting and measuring the bound substrate byelemental analysis.

Another aspect of the applicant's teachings is to provide a kit for thedetection and measurement of elements in a sample, where the measuredelements include element labels of uniquely labeled supports and anelement of a metal ion coordination complex, comprising: a multitude ofnon-phosphorylated substrates; uniquely labeled supports; metal ioncoordination complex; and optionally, kinase; kinase buffer; and ATP.The kit can further comprise instructions for i) immobilizing thenon-phosphorylated substrates on element labeled supports in separatesolutions; ii) incubating kinase in kinase buffer with the multitude ofnon-phosphorylated substrates immobilized on uniquely labeled supports,iii) incubating the metal ion coordination complex in the kinase bufferwith the kinase and the multitude of non-phosphorylated substratesimmobilized on uniquely labeled supports, iv) washing and separatingbound substrate from unbound substrate; v) measuring the metal ioncoordination complex bound to the multitude of phosphorylated substrateimmobilized on uniquely labeled supports by elemental analysis.

Another aspect of the applicant's teachings is to provide a kit for thedetection and measurement of elements in a sample, where the measuredelements include element tags attached to affinity products thatrecognize phosphorylated substrates, comprising: non-phosphorylatedsubstrate ready to be introduced into a cell; and an element tag fordirectly tagging an affinity product; and optionally an affinityproduct. The kit can further comprise instructions for i) introducingthe non-phosphorylated substrate into a cell; ii) directly tagging anaffinity product that recognizes phosphorylated substrates; iii) fixingand permeabilizing the cells; iv) combining the labeled affinity productwith the cells; v) separating bound affinity product from unboundaffinity product, and vi) detecting and measuring the amount of thebound affinity product labeled with an element tag by particle elementalanalysis.

Another aspect of the applicant's teachings is to provide a kit for thedetection and measurement of elements in a sample, where the measuredelements include an element tag attached to a phosphorylated substrateand a metal ion coordination complex, comprising: an element tag fordirectly tagging phosphorylated substrate; phosphorylated substrate; asolid support; metal ion coordination complex; and optionally,phosphatase; phosphatase buffer and ADP. The kit can further compriseinstructions for i) direct tagging of the phosphorylated substrate withan element tag; ii) attaching the metal ion coordination complex to thesupport; iii) incubating the element labeled phosphorylated substratewith the support with attached metal ion coordination complex; iv)separating bound substrate from unbound substrate; v) incubating thephosphatase in phosphatase buffer with the support with the attachedmetal ion coordination complex; vi) separating bound substrate fromunbound substrate; vii) eluting the bound substrate, and viii) measuringthe bound substrate by solution elemental analysis.

Another aspect of the applicant's teachings is to provide a kit for thedetection and measurement of elements in a sample, where the measuredelements include an element tag attached to a phosphorylated substrate,an element of a metal ion coordination complex, and elements of uniquelylabeled supports, comprising: an element tag for directly taggingphosphorylated substrate; a multitude of phosphorylated substrates;uniquely labeled supports; metal ion coordination complex; andoptionally, phosphatase, phosphatase buffer and ADP. The kit can furthercomprise instructions for i) direct tagging the phosphorylatedsubstrates with an element tag; ii) attaching a metal ion coordinationcomplex to the uniquely labeled support; iii) adding element labeledphosphorylated substrates to the uniquely labeled support with attachedmetal ion coordination complex in separate volumes, iv) incubating thesubstrates; v) washing the supports; vi) combining the multitude ofuniquely labeled supports having attached thereto the multitude ofresultant phosphorylated substrate labeled with an element tag throughcoordination to the metal ion coordination complex that is attached tothe supports; vii) incubating the phosphatase, the phosphatase bufferand the supports; viii) separating bound substrate from unboundsubstrate; and ix) measuring the phosphorylated substrate labeled withan element tag coordinated to the metal ion coordination complexattached to said multitude of uniquely labeled supports by particleelemental analysis.

BRIEF DESCRIPTION OF THE FIGURES

The invention is illustrated in the figures, which are meant to beexemplary and not limiting.

FIG. 1. Dose-dependence curve of EGFR kinase activity. Increasingamounts of EGFR-GST were incubated with 2 ug biotinylated substratepeptide (PTP1B) per reaction per well of 96-well streptavidin coatedplate. All reactions were set up in triplicate. Detected signal ispresented as normalized response of Ti ions to Ir internal standard.

FIG. 2. Peptide concentration dependence of EGFR kinase activity.Increasing amounts of biotinylated substrate peptide (PTP1B) wereincubated with 50 ng of EGFR-GST per reaction per well of 96-wellStreptavidin coated plate. All reactions were set up in triplicate.Detected signal is presented as normalized response of Ti ions to Irinternal standard.

FIG. 3. Intracellular EGFR kinase activity in human cells. Lysatesprepared from A431 and KG1-a cells were mixed with PTP1B(Tyr66)substrate linked to agarose beads in the presence of ATP and cations.Washed agarose beads with phosphorylated substrate were incubated withTi02 particle suspension. Analysis of titanium content in solution wasdone by ICP-MS. Triplicate samples were set up for analysis.

FIG. 4. Schematic representation of solution ICP-MS analysis of kinaseactivity in cellular lysates, in accordance with the invention.

FIG. 5. Flow chart showing method of specific kinase(s) assay, inaccordance with the invention.

FIG. 6. Flow chart showing method of specific phosphatase(s) assay, inaccordance with the invention.

FIG. 7. Flow chart showing method of specific kinase(s) assay usinguniquely labeled beads, in accordance with the invention.

FIG. 8. Flow chart showing method of specific phosphatase(s) assay usinguniquely labeled beads, in accordance with the invention.

DESCRIPTION OF THE VARIOUS EMBODIMENTS

The present invention comprises use of elemental tags. The choice of theelement to be employed in the methods of the applicant's teaching ispreferably selected on the basis of its natural abundance in the sampleunder investigation and whether the element is toxic to the sample underinvestigation.

Most metals of the transition and rare earth groups are anticipated foruse in applicant's teaching. It is wise to choose elements that have lowor no cytotoxicity and have a low abundance in growth media andbiological samples. For example, vanadium and mercury can be toxic tocertain cells, while Fe, Cu and Zn can be present in high concentrationsin some cell culture media. On the other hand, Pr, Ho, Tb, La, forexample are normally well tolerated by mammalian cells and are notabundant in the environment.

An unusual isotope composition of the tag element can be used in orderto distinguish between naturally present elements in the sample and thetag material. It is advantageous if the relative abundance of the tagelements is sufficiently different from the relative abundance ofelements in a given sample under analysis. By “sufficiently different”it is meant that under the methods of the present invention it ispossible to detect the target elemental tag over the background elementscontained in a sample under analysis. Indeed, it is the difference ininter-elemental ratios of the tagging elements and the sample matrixthat can be used advantageously to analyze the sample.

It is feasible to select elemental tags, which do not produceinterfering signals during analysis (i.e. do not have over-lappingsignals due to having the same mass). Therefore, two or more analyticaldeterminations can be performed simultaneously in one sample. Moreover,because the elemental tag can be made containing many copies of the sameatoms, the measured signal can be greatly amplified.

Aspects of the Applicant's teachings may be further understood in lightof the following examples, which should not be construed as limiting thescope of the present teachings in any way.

Epidermal growth factor receptor (EGFR) is a 170 kDa tyrosine kinase.Ligand binding results in receptor dimerization, autophosphorylation onnumerous tyrosine residues, activation of downstream signaling andlysosomal degradation.

Phosphorylation of Tyr845 in the kinase domain may stabilize theactivation loop, maintaining the enzyme in an active state and provide abinding surface for substrate proteins. c-Src is involved inphosphorylation of Tyr845. Phosphotyrosine 992 is a direct binding sitefor the PLC-g SH2 domain, resulting in activation of PLC-g mediateddownstream signaling. Phosphorylation of Tyr1045 creates a major dockingsite for c-Cbl. Binding of c-Cbl to the activated EGFR leads to receptorubiquitination and degradation. Phospho-Tyr1068 of activated EGFR is adirect binding site for Grb2. Phospho-tyrosine 1148 and 1173 provide adocking site for SHC. Both sites are involved in the activation of MAPkinase signaling. Phosphorylation of EGFR on serine and threonineresidues attenuates EGFR kinase activity. Ser1046/1047 in thecarboxy-terminal region of EGFR are sites phosphorylated by CaM kinaseII. Mutations of Ser1046/1047 upregulate tyrosine autokinase activity ofEGFR. EGFR is highly expressed by A431 epidermoid carcinoma cells (atleast 1e6 receptors per cell) and is partly responsible for the activeproliferation of these cells.

Experiment 1. In one embodiment, in vitro titration assay forrecombinant EGFR kinase and substrate were developed using ICP-MS.

To probe activity of recombinant EGFR, expressed as a GST-kinase fusionprotein (EGFR-GST Cell Signaling Tech.#7908), an ICP-MS assay wasdevised using a biotinylated peptide substrate PTP1B(Tyr66) (CellSignaling Tech.#1325) and 5% Ti0₂ particle suspension in water (Sigma#643114). Streptavidin coated 96-well plates (Sigma #M5432) wereincubated with 2 ug biotinylated PTB1B in kinase buffer (1× KinaseBuffer: 25 mM Tris-HCl (pH 7.5), 5 mM β-glycerophosphate, 2 mMdithiothreitol (DTT), 0.1 mM Na3VO4, 10 mM MgCl2) and 200 mM ATP, towhich various amounts of EGFR-GST were added. All reactions were set upin triplicate. The kinase reaction was stopped after 30 minutesincubation with 50 mM EDTA and all wells were washed 6 times withbuffered saline. Thus, only phosphorylated PTP1B(Tyr66) attached to thesupport through biotin-streptavidin binding remained in the wells. Forphosphorylation event detection, a solution of Ti0₂ diluted amillion-fold from the stock 5% in buffered saline was added for bindingwith phosphate residues on Tyr66. Finally, wells were washed 6 timeswith buffered saline, and filled with 80 uL concentrated HCl (SeaStarInc) per well, and an equal volume of 1 ppb Ir standard was added forfurther solution analysis by ICP-MS. Results are presented in FIG. 1.The results show that GST-kinase activity follows a dose-dependencecurve with the maximum activity at 50 ng of kinase per 2 microg ofsubstrate.

Antagonists and agonists of the enzyme can also be added to theincubation mix. The support can be labeled particles or beads. Theactive enzyme can be in the form of a cell lysate.

In another embodiment, phosphatase instead of kinase is used as theactive enzyme. For example, a solution of free phosphorylated substratelabeled with an element tag can be incubated with a support havingattached thereto a metal ion coordination complex. Free phosphorylatedsubstrate can be separated from the bound phosphorylated substrate bymethods known to those skilled in the art. ADP and at least onephosphatase can then be incubated with the support under conditions toenable the phosphatase to dephosphorylate the substrate. The freesubstrate can be removed from the bound substrate and the free substratecan be analyzed by elemental analysis.

Antagonists and agonists of the enzyme can also be added to theincubation mix. The support can be labeled particles or beads. Theactive enzyme can be in the form of a cell lysate.

Experiment 2. In another embodiment, experiments were designed to probethe peptide concentration dependence of the kinase. The conditions weresimilar to those describe above except that the amount of GST-EGFR waskept constant at 50 ng per well, while the amounts of PTP1B substratewere varied. Results are shown in FIG. 2. Likewise, the amount ofsubstrate significantly influences the kinase reaction, with 1 microgsubstrate eliciting a response half of the maximal at 2 microg.

Experiment 3. Another embodiment of the invention is related to EGFRkinase activity in human cell lines analyzed by ICP-MS. The adherentA431 cell line was cultured at 70% confluence in alpha-MEM medium(Invitrogen) supplemented with L-glutamine, penicillin-streptomycin, and10% fetal bovine serum at 37° C. under 5% CO₂. Cells were placed on iceand rinsed twice with cold (4° C.) phosphate buffered saline and 400 ulof cell lysis buffer (Cell Signaling #9803) plus phosphatase andprotease inhibitors were added to each 100 mm plate. Plate contents werecollected by scraping with a plastic cell scraper. The lysate wastransferred to a 1.5 ml Eppendorf tube on ice and then clarified at100,000×g for 15 minutes at 4° C. The suspension grown KG1-a cells werewashed with cold buffer by low speed centrifugation (300×g for 10minutes) and the cell pellet were lysed similar to A431 cells Proteinconcentration of lysates was determined using the NanoDrop Inc. system.Lysates from the two cell lines were adjusted with lysis buffer to thesame protein concentration. KG1-a leukemia cell line does not expressEGFR and was used as a negative control for the assay. A431 cells areknown to synthesize large amounts of the kinase. The cell lysates weremixed with kinase buffer (Cell Signaling Tech.#9803), 200 mM ATP andagarose-substrate slurry PTP1B(Tyr66) (SignalScout EGFR-substrate onagarose, Stratagene #206307). For positive control, triplicate samplesof EGFR-GST kinase (50 ng/sample as described above) were set up insteadof the lysate. Negative controls contained the equivalent amount ofkinase buffer instead of lysate or kinase. Incubations were carried outat 37° C. for 30 minutes, after which the agarose beads (3 um indiameter according to the manufacturer) were pelleted by low speedcentrifugation (500×g, 10 min) and washed 3 times with buffered saline.A 0.0005% suspension of Ti02 particles was added to each sample andincubated for 30 minutes. Thus, the phosphorylated Tyr66 of thePTP1B-agarose substrate interacted with the surface chemistry of Ti02and bound the titanium particles to the agarose beads. Schematicrepresentation of this process is given in FIG. 4 and a general workflow chart is shown in FIG. 7. Further washing of agarose beads ensuresthat only specifically bound titanium particles remain in the samples.Finally, pelleted material was dissolved in concentrated HCl, mixed withan equal amount of 1 ppb Ir internal standard and analyzed by solutionICP-MS. Results are presented in FIG. 3. As evident from the data, onlylysates obtained from A431 cells showed a significant response even atthe lowest amount of lysate tested (5 ul), while the negative KG1-a cellline did not show EGFR kinase activity at the highest loading.Therefore, the assay may be used to quantify the activity of a knownkinase in cellular lysates without the need of usinganti-phosphotyrosine antibodies or radioactively labeled reagents.

Experiment 4. In yet a further embodiment, the invention is related toactivity of phosphoinositide-3 kinase (PI 3-kinase) and analysis of Aktphosphorylation and utilized culture conditions in which the cells wereserum starved, prior to stimulation with a specific growth factor(PDGF). The PI 3-kinase is a lipid kinase, phosphorylating the 3-OH ofphosphatidylinositol-4,5-bisphosphate. In vitro substrates for PI3K canbe L-α-phosphatidylinositol, La-phosphatidylethanolamine,L-α-phosphatidyl-L-serine, L-α-lysophosphatidylcholine and sphingomyelinto name a few. The generation of this signaling lipid by PI 3-kinase isin response to growth factor tyrosine kinase receptor stimulation (forexample by PDGF) recruiting PI 3-kinase (consisting of the p85regulatory domain and the p110 catalytic domain) to the plasma membrane,thereby activating lipid kinase activity. The signaling lipid,phosphatidylinositol-3,4,5-triphosphate (PIP3), recruits kinases thatcontain pleckstrin homology domains (PH) to the plasma membrane. Theseinclude Pdk1, Akt, Tec/Btk tyrosine kinases and Grp1. Pdk1 is aconstitutively active kinase whose activity is regulated by localizationwith target proteins through recruitment to the plasma membrane, or inthe case of PKC kinases, through interaction with the PIF binding domainon Pdk1. Pdk1 also activates Akt through phosphorylation. There are anumber of targets for Akt, including FKHR, GSK-3, Bad and caspase-9. Arole for PI 3-kinase in cancer is suggested by studies that show thatthe protein levels are increased in some tumors and throughidentification of a mutation in the PTEN tumor suppressor gene. PTEN isa lipid phosphatase that negatively regulates the amount of PIP3 in thecell. Loss of PTEN function leads to cell proliferation and growththrough enhanced stimulation of the downstream targets of the PI3-kinase pathway. As PIP3 is the direct product of PI 3-kinase,inhibition of this enzyme would similarly reduce the level of PIP3 inthe cell and reduce cell growth and proliferation, regardless of thestatus of PTEN. Inhibitors of PI 3-kinase have been identified, the bestknown being wortmannin and LY294002. Wortmannin has been shown to be notspecific for PI 3-kinase. In a recent study, LY294002 was shown toinhibit one other known kinase (casein kinase II), so it may be morespecific than wortmannin.

Cell line and culture. A2780 ovarian cancer cell line is cultured inRPMI medium (Gibco) supplemented with L-glutamine, insulin (10 ug/ml),and 10% fetal bovine serum at 37° C. under 5% CO₂. For kinasestimulation 23-24 hour after initiating serum-starvation, the cells aretreated with PDGF BB (R&D Systems #220 BB at 10 ng/ml) or control bufferin serum- and supplement-free media with or without inhibitor (25 uMLY294002) or DMSO for 15 minutes. Once the treatment is concluded, thecells are placed on ice and rinsed twice with cold (4° C.) TBS. Cellsare collected by scraping with a plastic cell scraper. The pellet islysed in cell lysis buffer plus inhibitors (see below). The lysate istransferred to a 1.5 ml Eppendorf tube on ice and then clarified at100,000×g for 15 minutes at 4° C. Aliquots of cell lysate containingactivated kinase of interest is reacted with element-labeled specificsubstrates attached to a solid support.

In one embodiment, to assay the activity of PI3K the synthetic lipidbiotin-phosphatidylinositol 3,4,5-triphosphate (biotin-PtdIn (3,4,5)P3)from C39B6 Echelon BioSciences Inc. is reacted with a streptavidincoated 96-well plate (SigmaScreen #M5432) to produce a monolayer ofsubstrate attached to the bottom of the wells to which cell lysatesprepared as described above are added. Short incubation for 30 minutesand subsequent washes with Tris buffered saline (TBS) yield PtdIn(3,4,5)P3 phosphorylated by activated cellular PI3K. If cells areincubated with the LY294002 inhibitor prior to PDGF stimulation, thenthe PtdIn (3,4,5)P3 is not phosphorylated in the designated wells.Finally, Ti02 in kinase buffer is added to all the wells and after abrief wash concentrated HCl is used to dissolve the biomolecules forsolution elemental analysis, for example ICP-MS, to determine theabsolute amount of titanium.

Experiment 5. In another embodiment, uniquely labeled beads coated withstreptavidin are reacted with biotinylted peptide substrates such thateach peptide substrate corresponds to one type of labeled bead. Forexample, Akt substrate with sequence biotin-PRPAATF, GSK-3 substratewith sequence biotin-YRRAAVPPSPSLSRHSSPHQ(pS)EDEEE, PDK1 substrate withbiotinKTFCGTPEYLAPEVR-REPRILSEEEQEMFRDFDYIADW, and PKC substrate withsequence biotin-QKRPSQRSKYL (JPT Peptide Technologies GmbH) can be usedfor the A2780 stimulated cell system. These labeled beads with peptidesubstrates in kinase buffer are incubated with cell lysates obtained asdescribed above. After washing by low speed centrifugation (10,000 rpm10 min in microcentrifuge), the beads are treated with 0.0005% solutionof Ti02 particles. The titanium particles bind to phosphate groups whichare attached to the peptides by specific kinases present in the celllysate. The reaction mixture with beads is once again washed by lowspeed centrifugation and the beads are analysed by elemental analysisparticle analysis in the flow cytometric mode. Beads that carry signalsof the unique elemental bead identifier together with the titaniumparticles indicate that the kinase of interest is present and active inthe cell. If inhibitors for a specific kinase are used (LY294002 for Aktfor example) during cell cultivation then there will be no concomitantTi present for the uniquely labeled bead with the Akt substrateattached.

Experiment 6. In yet another embodiment cells grown in culture areexposed to non-phosphorylated element-labeled peptides (Akt and PKAsubstrates, for example) conjugated with a PTD (protein transfer domain)sequence which enables the peptides to be taken up into the cytoplasm oflive cells. Otherwise the element-labeled kinase substrates can bemicroinjected into the cells, encapsulated into lipid microsomes whichare taken up by the cells or transferred into the live cells by othermeans known in the art. The cells are then stimulated with a specificligand, PDGF in the example above, fixed and permeabilized in order forantibodies labeled with a different element to gain access to thephosphorylated labeled substrates in the cells. For example, an antibodyor other affinity product labeled with Eu (europium) againstphospho(Thr)Akt substrate (PerkinElmer AD0184) together with anantibody/affinity product to phospho(Thr)PKA substrate labeled with Sm(samarium) can be used. Single cell particle analysis by the flowelemental analysis (for example, flow-ICP-MS) instrument quantitativelydetects levels of kinase activity in each cell according to theirelemental signals.

Experiment 7. In yet another embodiment, purified kinases or kinases incell lysates are mixed with kinase substrates labeled with elementaltags in kinase reaction buffer. This is followed by the addition ofbeads with Ga3+ ions exposed on the bead surface or with titanium oxidebeads that are known to bind specifically phosphate groups. Washing inbuffers and low speed centrifugation will yield beads that have capturedphosphorylated peptides of kinases that were active towards certainsubstrates. Single particle analysis by flow ICP-MS gives quantitativeresults of the kinase reaction.

Cell Lysis buffer (example): 20 mM Tris, pH 7.5, 150 mM NaCl, 1.0% NP40(v/v), 0.5% NaDOC, 0.1 mM MgCl2, 0.2 mM AEBSF, 1.5 microg/ml Aprotinin,1.0 microg/ml Leupeptin, 2.0 microM Pepstatin, 50 mM NaF, 1.0 mM Na3VO4.

Experiment 8. Normal phosphatase function is essential for maintainingcellular homeostasis. Dysfunction lies at the basis of numerous diseasesincluding tumorigenesis, thereby making phosphatases potential targetsfor therapeutic drugs. For example, the protein and lipid phosphatasePTEN has been associated with cancer. It is a tumor suppressor and itsloss permits constitutive signaling through the PI3K pathway and thismay lead to the development of a tumor. In cells with low PTEN, thereare elevated levels of PtdIn(3,4,5)P3 which acts as a second messengerto promote oncogenesis. PTEN hydrolyzes phosphate at the 3 position onthe inositol ring of PtdIn(3,4,5)P3 and Ins(1,3,4,5)P4, however thehighest catalytic activity in vitro has been observed with thenegatively charged, multiply phosphorylated polymer of (Glu-Tyr)n.

Protein phosphatases can be studied as purified enzymes or in thecontext of cell lysates. However, the cell lysis buffer in this caseshould not contain phosphatase inhibitors such as sodium vanadate orsodium fluoride. An excellent substrate for the mammalian PTP-1Bphosphatase is the peptide from an autophosphorylation site (tyr-992) ofthe epidermal growth factor receptor(EGFR)-Asp-Ala-Asp-Glu-pTyr-Leu-Ile-Pro-Gln-Gln-Gly (Biomol Inc,#P323-0001). In a solid support experiment, the PTP-1B phosphorylatedsubstrate is immobilized on a surface (microtiter plate or polystyrenebead) and reacted with the phosphatase (purified or as a cell lysate) ina phosphatase reaction buffer. Following washes, Ga³⁺ coordinationcomplex is added to the wells (see flow chart FIG. 6); high phosphataseactivity will be detected as a low signal for Ga3+ ions, whereas lowphosphatase activity will have a strong Ga signal. Embodiments whenphosphorylated substrates are attached to uniquely elemental labeledbeads reacted with the specific mix of phosphatases and TiO₂ particlesare also envisaged (included in flow chart FIG. 8).

Experiment 9

Another embodiment is a. method for a phosphatase assay, comprising:incubating ADP and at least one phosphatase, with an immobilizedphosphorylated substrate with attached metal ion coordination complex inconditions that enable the phosphatase to dephosphorylate the substrate;separating the free metal ion coordination complex from the immobilizednon-phosphorylated substrate and the immobilized phosphorylatedsubstrate with attached metal ion coordination complex; eluting themetal ion coordination complex into a solution; and measuring thesolution by elemental analysis.

Experiment 10

Another embodiment is a method for a phosphatase assay, comprising:incubating ADP, at least one phosphatase, and a multitude ofphosphorylated substrates with attached metal ion coordination compleximmobilized to element labeled supports in such manner that a singletype of phosphorylated substrate is attached to a single type of elementlabeled support in conditions that enable the phosphatase todephosphorylate the phosphorylated substrates; separating the free metalion coordination complex from the multitude of non-phosphorylatedsubstrates immobilized to element labeled supports and the multitude ofimmobilized phosphorylated substrate; and measuring the metal ioncoordination complex attached to said residual multitude ofphosphorylated substrate immobilized to uniquely labeled supports byelemental analysis. This allows the measurement of the bead's elementalsignal. For example, less signals from the metal coordination complexthan prior to phosphatase addition will indicate the level of enzymeactivity.

Kits:

Also provided are kits comprising components to practice the methods ofthe invention.

A kit is provided for the detection and measurement of elements in asample, where the measured elements include an element tag attached to anon-phosphorylated substrate and a metal ion coordination complex,comprising: an element tag for directly tagging non-phosphorylatedsubstrate; non-phosphorylated substrate; a solid support; metal ioncoordination complex; and optionally, kinase; kinase buffer; and ATP.The kit can further comprise instructions for i) directly tagging thenon-phosphorylated substrate with an element tag; ii) incubating kinasewith element labeled non-phosphorylated substrate in kinase buffer, iii)attaching metal ion coordination complex to the support; iv) addition ofsaid mixture to support with attached metal ion coordination complex vi)separating bound substrate from unbound substrate; vii) eluting thebound substrate, and viii) detecting and measuring the bound substrateby elemental analysis. The kit can further comprise a non-phosphorylatedsubstrate, wherein the non-phosphorylated substrate is directly labeledwith an element tag. The kit can further comprise a multitude ofnon-phosphorylated substrates directly labeled with unique element tags.The support with attached metal ion coordination complex can be atitanium oxide bead. The kit can further comprise a support with anattached metal ion coordination complex.

Also provided, is a kit for the detection and measurement of elements ina sample, where the measured elements include element labels of uniquelylabeled beads and an element of a metal ion coordination complex,comprising: a multitude of non-phosphorylated substrates; uniquelylabeled beads; metal ion coordination complex; and optionally, kinasebuffer; and ATP. The kit can further comprise instructions for i)immobilizing the non-phosphorylated substrates on element labeled beadsin separate solutions; ii) incubating kinase in kinase buffer with themultitude of non-phosphorylated substrates immobilized on uniquelylabeled beads, iii) incubating the metal ion coordination complex withthe multitude of phosphorylated substrates immobilized on uniquelylabeled beads, iv) washing and separating bound substrate from unboundsubstrate; v) measuring the metal ion coordination complex bound to themultitude of phosphorylated substrate immobilized on uniquely labeledbeads by elemental analysis. The kit can further comprise a multitude ofnon-phosphorylated substrates immobilized on uniquely labeled beads.

Also provided is a kit for the detection and measurement of elements ina sample, where the measured elements include element tags attached toaffinity products that recognize phosphorylated substrates, comprising:non-phosphorylated substrate ready to be introduced into a cell; and anelement tag for directly tagging the affinity product. The kit canfurther comprise instructions for i) introducing the non-phosphorylatedsubstrate into a cell; ii) directly tagging affinity products thatrecognize phosphorylated substrates; iii) fixing and permeabilizing thecells; iv) combining the labeled affinity product with the cells; v)separating bound affinity product from unbound affinity product and vi)detecting and measuring the amount of the bound affinity product labeledwith an element tag by particle elemental analysis. The kit can furthercomprise a multitude of non-phosphorylated substrates to be introducedinto a cell. The non-phosphorylated substrate with or without an elementtag can be in a sterile solution at a concentration compatible withmicroinjection into the cell. The kit can further comprise an antibodyor affinity product that recognizes phosphorylated substrates, whereinthe antibody or affinity product is directly labeled with an elementtag. There are many antibodies or affinity products. The kit can furthercomprise an expression plasmid and wherein the non-phosphorylatedsubstrate is produced by an expression plasmid transfected orelectroporated into the cell. The non-phosphorylated substrate with orwithout an element tag can be in a liposome solution. The affinityproduct that recognizes the phosphorylated substrates can be selectedfrom a group consisting of antibody, Fab′, aptamer, antigen, hormone,growth factor, receptor, protein, peptide, SH2 peptide, and nucleicacid.

Also provided is a kit for the detection and measurement of elements ina sample, where the measured elements include an element tag attached toa phosphorylated substrate and a metal ion coordination complex,comprising: an element tag for directly tagging phosphorylatedsubstrate; phosphorylated substrate; a solid support; metal ioncoordination complex; optionally, phosphatase; phosphatase buffer andADP. The kit can further comprise instructions for i) direct tagging ofthe phosphorylated substrate with an element tag; ii) attaching themetal ion coordination complex to the support; iii) incubating theelement labeled phosphorylated substrate with the support with attachedmetal ion coordination complex; iv); washing of the support; v)incubating the phosphatase in phosphatase buffer with the support withthe attached metal ion coordination complex; vi) separating boundsubstrate from unbound substrate; ix) eluting the bound substrate, andx) measuring the bound substrate by solution elemental analysis. Thesupport with attached metal ion coordination complex can be a titaniumoxide bead. The kit can further comprise a support with attached metalion coordination complex. The kit can further comprise a phosphorylatedsubstrate which can be directly labeled with an element tag. The kit canfurther comprise a multitude of phosphorylated substrates directlylabeled with unique element tags. Finally, the kit can compriseinstructions for the solution to be analyzed by solution elementalanalysis.

Also provided is a kit for the detection and measurement of elements ina sample, where the measured elements include an element tag attached toa phosphorylated substrate, an element of a metal ion coordinationcomplex, and elements of uniquely labeled beads, comprising: an elementtag for directly tagging phosphorylated substrate; a multitude ofphosphorylated substrates; uniquely labeled beads; metal ioncoordination complex; optionally, phosphatase; phosphatase buffer andADP. The kit can further comprise instructions for i) direct tagging thephosphorylated substrates with an element tag; ii) attaching a metal ioncoordination complex to the uniquely labeled bead; iii) adding elementlabeled phosphorylated substrates to the uniquely labeled bead withattached metal ion coordination complex in separate volumes, iv)incubating the substrates; v) washing the beads; vi) combining themultitude of uniquely labeled beads having attached thereto themultitude of resultant phosphorylated substrate labeled with an elementtag through coordination to the metal ion coordination complex that isattached to the beads; vii) incubating the phosphatase, the phosphatasebuffer and the beads; viii) separating bound substrate from unboundsubstrate; x) measuring the phosphorylated substrate labeled with anelement tag coordinated to the metal ion coordination complex attachedto said multitude of uniquely labeled beads by particle elementalanalysis. The kit can further comprise a multitude of phosphorylatedsubstrates directly labeled with the same element tag or unique elementtags. The kit can further comprise a multitude of uniquely labeled beadswith attached metal ion coordination complex. The non-phosphorylatedsubstrate with or without an element tag can be attached to a proteintransfer domain (PTD) in a sterile solution. The kit can compriseinstructions for a cell lysate to be incubated wherein the cell lysatecomprises a phosphatase.

In the kits described above the element can be measured using a massspectrometer. The element can be an isotope or ion. The element can beselected from a group consisting of the noble and transition metals,lanthanides, rare earth elements, gold, silver, platinum, rhodium,iridium and palladium. The element can include more than one atom of anisotope. The kits can further comprise standards, a dilution buffer, anelution buffer, a wash buffer and/or an assay buffer. Instructions forparticle elemental analysis can also be included.

The kits can also include the following reagents:

(i) Protein kinase substrate labeled with element tag

(ii) Lipid kinase substrate labeled with element tag

(iii) Uniquely labeled beads with attached metal ion coordinationcomplex

(iv) Uniquely labeled beads attached to kinase substrate

(v) Uniquely labeled beads attached to phosphatase substrate

(v) Protein phosphatase substrate labeled with element tag

(vi) Lipid phosphatase substrate labeled with element

While the Applicant's teachings are described in conjunction withvarious embodiments, it is not intended that the Applicant's teachingsbe limited to such embodiments. On the contrary, the Applicant'steachings encompass various alternatives, modifications, andequivalents, as will be appreciated by those of skill in the art.

All references cited in the disclosure are herein incorporated byreference.

REFERENCE LIST

-   1. Noland, B. Determining phosphorylating activity of enzyme, by    combining enzyme with phosphorylatable compound labeled with    acceptor fluorophore, ATP analog, and donor fluorophore, and    measuring fluorescence resonance energy transfer. STRUCTURAL GENOMIX    INC and Noland, B. [WO2004059291-A2; US2004146961-A1;    AU2003300363-A1].-   2. Xue, Q.; Gibbons, I. Multiplexed enzyme assay comprises    performing enzyme reactions in presence of substrates to convert    substrate to product, separating them, detecting their separation    characteristic and determining amount of product.-   3. Saxinger, C. Automated peptide synthesis—using novel solvent    resistant substrates and novel solns. for storing protected carboxyl    terminal aminoacid(s). US DEPT HEALTH & HUMAN SERVICE, US SEC OF    COMMERCE, and US NAT INST OF HEALTH. [U.S. Pat. No. 7,398,458-N;    WO9102714-A; AU9061859-A; U.S. Pat. No. 6,031,074-A].-   4. Crouch, S. P. M.; Slater, K. J. Measuring protein kinase    activity, involves adding substrate to a solution with ATP and    kinase, and another solution with ATP alone, and measuring ATP    and/or ADP concentration using a bioluminescence reaction.-   5. Hackel, P. O.; Zwick, E.; Prenzel, N.; Ullrich, A. Epidermal    growth factor receptors: critical mediators of multiple receptor    pathways Current Opinion in Cell Biology 1999, 11, 184-89.-   6. Cooper, J. A.; Howell, B. The When and How of Src Regulation Cell    1993, 73, 1051-54.-   7. Schlosser, A.; Vanselow, J. T.; Kramer, A. Mapping of    phosphorylation sites by a multi-protease approach with specific    phosphopeptide enrichment and nanoLC-MS/MS analysis Analytical    Chemistry 2005, 77, 5243-50.-   8. Meyer, T. J.; Meyer, G. J.; Pfennig, B. W.; Schoonover, J. R.;    Timpson, C. J.; Wall, J. F.; Kobusch, C.; Chen, X. H.; Peek, B. M.;    Wall, C. G.; Ou, W.; Erickson, B. W.; Bignozzi, C. A.    Molecular-Level Electron-Transfer and Excited-State Assemblies on    Surfaces of Metal-Oxides and Glass Inorganic Chemistry 1994, 33,    3952-64.

1. A method for a kinase assay, comprising: a) Incubating ATP, at leastone kinase, and a free non-phosphorylated substrate labeled with anelement tag, with a support having attached thereto metal ioncoordination complexes under conditions to enable the kinase tophosphorylate the substrate; b) Separating free non-phosphorylatedsubstrate from bound phosphorylated substrate labeled with an elementtag to the support; c) Eluting the element tag associated with theresultant phosphorylated substrate into a solution; and d) Performingsolution elemental analysis of said solution.
 2. The method of claim 1where in step (a) a multitude of free non-phosphorylated substrates eachlabeled with a unique element tag are incubated.
 3. The method of claim1 wherein the metal ion coordination complex attached to the support isa titanium oxide bead.
 4. The method of claim 1 where in step (a) theconditions to enable the kinase to phosphorylate the substrate include akinase reaction buffer.
 5. The method of claim 1 where in step (a)antagonists or agonists of kinase are incubated.
 6. The method of claim1 wherein the kinase is delivered in the form of a cell lysate.
 7. Amethod for a phosphatase assay, comprising: a) Incubating freephosphorylated substrate labeled with an element tag with a supporthaving attached thereto metal ion coordination complexes; b) Separatingfree phosphorylated substrate from bound phosphorylated substratelabeled with an element tag attached to the metal ion coordinationcomplexes attached to the support; c) Incubating ADP and at least onephosphatase with the bound phosphorylated substrate labeled with anelement tag attached to the metal ion coordination complexes attached tothe support under conditions to enable the phosphatase todephosphorylate the substrate; d) Separating free non-phosphorylatedsubstrate labeled with an element tag from bound phosphorylatedsubstrate attached to the metal ion coordination complexes attached tothe support; e) Measuring the tag element in a solution of the freenon-phosphorylated substrate.
 8. The method of claim 7 wherein amultitude of free phosphorylated substrates each labeled with an elementtag that is characteristic of the substrate are incubated in step (a)and the tag elements characteristic of the substrate are measured instep (e).
 9. The method of claim 7 where in step (c) the conditions toenable the phosphatase to dephosphorylate the substrate includeincubation with a phosphatase reaction buffer.
 10. The method of claim 7where in step (c) antagonists or agonists of phosphatase are incubated.11. The method of claim 7 wherein the metal ion coordination complex isattached to element labeled beads.
 12. The method of claim 7 wherein themetal ion coordination complex attached to the support is a titaniumoxide bead.
 13. The method of claim 7 wherein the phosphatase is in theform of a cell lysate.
 14. A method for a phosphatase assay, comprising:a) Incubating, in a multitude of solutions, each solution comprising adifferent free phosphorylated substrate labeled with an element tag,which can optionally be the same element tag for all substrates, aplurality of element labeled supports having attached thereto a metalion coordination complex, in such manner that each type ofphosphorylated substrate labeled with an element tag, which canoptionally be the same element tag for all substrates, is attached to asingle type of element labeled support; b) Separating freephosphorylated substrate from the bound substrate attached to the metalion coordination complex attached to the multitude of element labeledsupports in the multitude of separate solutions; c) Incubating themultitude of element labeled supports having attached thereto themultitude of phosphorylated substrates labeled with an element tag,which can optionally be the same element tag for all substrates, throughattachment to the metal ion coordination complex that is attached to thesupports in a single solution with ADP and at least one phosphatase inconditions that enable the phosphatase to dephosphorylate thephosphorylated substrates; d) Separating free non-phosphorylatedsubstrate from bound phosphorylated substrate labeled with an elementtag, which can optionally be the same element tag for all substrates,attached to the metal ion coordination complex attached to saidmultitude of element labeled supports; e) Performing particle elementalanalysis of bound phosphorylated substrate labeled with an element tag,which can optionally be the same element tag for all substrates,attached to the metal ion coordination complex attached to the multitudeof element labeled supports.
 15. A method for a kinase assay,comprising: a) Incubating ATP, at least one kinase, and a free metal ioncoordination complex, with an immobilized non-phosphorylated substrateunder conditions which enable the kinase to phosphorylate the substrate;b) Separating immobilized phosphorylated substrate attached to the metalion coordination complex from the free ion coordination complex and theimmobilized non-phosphorylated substrate; c) Eluting the metal ioncoordination complex attached to the immobilized phosphorylatedsubstrate into a solution; and d) Measuring the solution by elementalanalysis
 16. A method for a kinase assay, comprising: a) Incubating ATP,at least one kinase, a free metal ion coordination complex, and amultitude of non-phosphorylated substrates immobilized on elementlabeled supports in such manner that a single type of non-phosphorylatedsubstrate is attached to a single type of element labeled support, inconditions to enable the kinase to phosphorylate the substrates; b)Separating the multitude of phosphorylated substrates immobilized onelement labeled supports having attached metal ion coordination complexfrom the free metal ion coordination complexes and the multitude ofimmobilized non-phosphorylated substrates; and c) Measuring themultitude of phosphorylated substrate immobilized on element labeledsupports having attached metal ion coordination complex by elementalanalysis.
 17. A method for a kinase assay, comprising: a) Introducing amultitude of non-phosphorylated substrates with element tags into livecells; b) Incubating the cells having the introduced non-phosphorylatedsubstrates with an agonist or an antagonist of kinase activity; c)Fixing and permeabilizing the cells; d) Incubating the cells withelement-labeled antibodies directed against phosphospecific kinasesubstrates; e) Separating the cells from unbound antibodies; f)Measuring the phosphorylated substrates with element tags and attachedelement-labeled antibodies by elemental analysis.
 18. The method ofclaim 17 wherein the step of introducing a multitude ofnon-phosphorylated substrates is selected from the group consisting ofmicroinjection, transfection of peptide expressing plasmid, liposomedelivery, and incubation with PTD-conjugated substrate.
 19. The methodof claim 17 wherein the step of separating the cells from the unboundantibodies is selected from the group consisting of low speedcentrifugation and filtration.
 20. The method of claim 17 wherein thenon-phosphorylated substrates are labeled with different element tags,specific to each substrate.
 21. The method of claim 17 wherein thenon-phosphorylated substrates are labeled with the same element tag. 22.A. method for a phosphatase assay, comprising: Incubating ADP and atleast one phosphatase, with an immobilized phosphorylated substrate withattached metal ion coordination complexes in conditions that enable thephosphatase to dephosphorylate the substrate; b) Separating the freemetal ion coordination complex from the immobilized non-phosphorylatedsubstrate and the immobilized phosphorylated substrate with attachedmetal ion coordination complex; c) Eluting the metal ion coordinationcomplex into a solution; d) Measuring the solution by elementalanalysis.
 23. A method for a phosphatase assay, comprising: a)Incubating ADP, at least one phosphatase, and a multitude ofphosphorylated substrates with attached metal ion coordination compleximmobilized to element labeled supports in such manner that a singletype of phosphorylated substrate is attached to a single type of elementlabeled support in conditions that enable the phosphatase todephosphorylate the phosphorylated substrates; b) Separating the freemetal ion coordination complex from the multitude of non-phosphorylatedsubstrates immobilized to element labeled supports and the multitude ofimmobilized phosphorylated substrate; and c) Measuring the metal ioncoordination complex attached to the multitude of phosphorylatedsubstrate immobilized to uniquely labeled supports by elementalanalysis.
 24. A kit for the detection and measurement of elements in asample, where the measured elements include an element tag attached to anon-phosphorylated substrate and a metal ion coordination complex,comprising: a) an element tag for directly tagging non-phosphorylatedsubstrate; b) non-phosphorylated substrate; c) a solid support; d) metalion coordination complex; e) and optionally, kinase; f) kinase buffer;and g) ATP.
 25. The kit of claim 24 further comprising instructions fori) directly tagging the non-phosphorylated substrate with an elementtag; ii) incubating kinase with element labeled non-phosphorylatedsubstrate in kinase buffer, iii) attaching metal ion coordinationcomplex to the support; iv) incubating the kinase with element labelednon-phosphorylated substrate in kinase buffer with the support havingattached metal ion coordination complex; v) separating bound substratefrom unbound substrate; vi) eluting the bound substrate, and vii)detecting and measuring the bound substrate by elemental analysis.
 26. Akit for the detection and measurement of elements in a sample, where themeasured elements include element labels of uniquely labeled supportsand an element of a metal ion coordination complex, comprising: a) amultitude of non-phosphorylated substrates; b) uniquely labeledsupports; c) metal ion coordination complex; d) and optionally, kinase;e) kinase buffer; and f) ATP.
 27. The kit of claim 26 further comprisinginstructions for i) immobilizing the non-phosphorylated substrates onelement labeled supports in separate solutions; ii) incubating kinase inkinase buffer with the multitude of non-phosphorylated substratesimmobilized on uniquely labeled supports, iii) incubating the metal ioncoordination complex in the kinase buffer with the kinase and themultitude of non-phosphorylated substrates immobilized on uniquelylabeled supports, iv) washing and separating bound substrate fromunbound substrate; v) measuring the metal ion coordination complex boundto the multitude of phosphorylated substrate immobilized on uniquelylabeled supports by elemental analysis.
 28. A kit for the detection andmeasurement of elements in a sample, where the measured elements includeelement tags attached to affinity products that recognize phosphorylatedsubstrates, comprising: a) non-phosphorylated substrate ready to beintroduced into a cell; and b) an element tag for directly tagging anaffinity product; and optionally c) an affinity product.
 29. The kit ofclaim 28 further comprising instructions for i) introducing thenon-phosphorylated substrate into a cell; ii) directly tagging anaffinity product that recognizes phosphorylated substrates; iii) fixingand permeabilizing the cells; iv) combining the labeled affinity productwith the cells; v) separating bound affinity product from unboundaffinity product, and vi) detecting and measuring the amount of thebound affinity product labeled with an element tag by particle elementalanalysis.
 30. A kit for the detection and measurement of elements in asample, where the measured elements include an element tag attached to aphosphorylated substrate and a metal ion coordination complex,comprising: a) an element tag for directly tagging phosphorylatedsubstrate; b) phosphorylated substrate; c) a solid support; d) metal ioncoordination complex; e) and optionally, phosphatase; f) phosphatasebuffer and g) ADP.
 31. The kit of claim 30 further comprisinginstructions for i) direct tagging of the phosphorylated substrate withan element tag; ii) attaching the metal ion coordination complex to thesupport; iii) incubating the element labeled phosphorylated substratewith the support with attached metal ion coordination complex; iv)separating bound substrate rom unbound substrate; v) incubating thephosphatase in phosphatase buffer with the support with the attachedmetal ion coordination complex; vi) separating bound substrate fromunbound substrate; vii) eluting the bound substrate, and viii) measuringthe bound substrate by solution elemental analysis.
 32. A kit for thedetection and measurement of elements in a sample, where the measuredelements include an element tag attached to a phosphorylated substrate,an element of a metal ion coordination complex, and elements of uniquelylabeled supports, comprising: a) an element tag for directly taggingphosphorylated substrate; b) a multitude of phosphorylated substrates;c) uniquely labeled supports; d) metal ion coordination complex; e) andoptionally, phosphatase f) phosphatase buffer and g) ADP.
 33. The kit ofclaim 32 further comprising instructions for i) direct tagging thephosphorylated substrates with an element tag; ii) attaching a metal ioncoordination complex to the uniquely labeled support; iii) addingelement labeled phosphorylated substrates to the uniquely labeledsupport with attached metal ion coordination complex in separatevolumes, iv) incubating the substrates; v) washing the supports; vi)combining the multitude of uniquely labeled supports having attachedthereto the multitude of resultant phosphorylated substrate labeled withan element tag through coordination to the metal ion coordinationcomplex that is attached to the supports; vii) incubating thephosphatase, the phosphatase buffer and the supports; viii) separatingbound substrate from unbound substrate; and ix) measuring thephosphorylated substrate labeled with an element tag coordinated to themetal ion coordination complex attached to said multitude of uniquelylabeled supports by particle elemental analysis.
 34. The kit of claim 32further comprising a multitude of phosphorylated substrates directlylabeled with the same element tag.
 35. The kit of claim 32 furthercomprising a multitude of phosphorylated substrates directly labeledwith unique element tags.
 36. The kit of claim 24 further comprising anon-phosphorylated substrate, wherein the non-phosphorylated substrateis directly labeled with an element tag.
 37. The kit of claim 24 furthercomprising a multitude of non-phosphorylated substrates directly labeledwith unique element tags.
 38. The kit of claims 24 or 30 where thesupport with attached metal ion coordination complex is a titanium oxidebead.
 39. The kit of claims 24 or 30 further comprising a support withan attached metal ion coordination complex.
 40. The kit of claim 26further comprising a multitude of non-phosphorylated substratesimmobilized on uniquely labeled beads.
 41. The kit of claim 28 furthercomprising a multitude of non-phosphorylated substrates to be introducedinto a cell.
 42. The kit of claim 28 wherein the non-phosphorylatedsubstrate with or without an element tag is in a sterile solution at aconcentration compatible with microinjection into the cell.
 43. The kitof claim 28 further comprising an affinity product that recognizesphosphorylated substrates, wherein the affinity product is directlylabeled with an element tag.
 44. The kit of claim, 28 further comprisinga multitude of affinity products that recognize phosphorylatedsubstrates, wherein the affinity products are directly labeled withunique element tags.
 45. The kit of claim 28 further comprising anexpression plasmid and wherein the non-phosphorylated substrate isproduced by an expression plasmid transfected or electroporated into thecell.
 46. The kit of claim 28 wherein the non-phosphorylated substratewith or without an element tag is in a liposome solution.
 47. The kit ofclaim 32 further comprising a multitude of uniquely labeled supportswith attached metal ion coordination complex.
 48. The kit of claim 30further comprising a phosphorylated substrate, wherein thephosphorylated substrate is directly labeled with an element tag. 49.The kit of claim 30 further comprising a multitude of phosphorylatedsubstrates directly labeled with unique element tags.
 50. The kit ofclaim 32 wherein the non-phosphorylated substrate with or without anelement tag is attached to a protein transfer domain (PTD) in a sterilesolution.
 51. A kit of any one of claims 25, 29 or 31 whereininstructions are provided for the solution to be analyzed by solutionelemental analysis after the second incubation without the separatingand eluting steps.
 52. A kit of claim 33 wherein instructions areprovided for a cell lysate to be incubated wherein the cell lysatecomprises a phosphatase.
 53. The kit of claim 24 wherein the element ismeasured using a mass spectrometer.
 54. The kit of claims 24 wherein theelement is an isotope or ion.
 55. The kit of claim 24 wherein theelement is selected from a group consisting of the noble metals,transition elements, lanthanides, rare earth elements, gold, silver,platinum, rhodium, iridium and palladium.
 56. The kit of claim 28wherein the affinity product that recognizes the phosphorylatedsubstrates is selected from a group consisting of antibody, Fab′,aptamer, antigen, hormone, growth factor, receptor, protein, peptide,SH2 peptide, and nucleic acid.
 57. The kit of claims 24 wherein theelement includes more than one atom of an isotope.
 58. The kit of claims24 further comprising any combination of the substances wherein thesubstances are selected from the group consisting of standards, adilution buffer, an elution buffer, a wash buffer and an assay buffer.59. The kit of claim 25 further comprising instructions for particleelemental analysis.